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Monday, April 27, 2009

The purported finding of DE* paraphyletic haplotypes in only 2 Tibetan sample candidates appears to have caused hysterical excitement in certain quarters, specifically amongst sects of individuals who are psychologically and emotionally tormented by the prospect of African ancestry in their "homelands". But this excitement is emotionally driven, and just that. As such, intellectual engagement gives way to religious cultism as the medium of self-expression. But let's just examine how much or what really lies herein that is worth being hysterically excited over:

DE* is a descendant clade of M168. M168 is undoubtedly African; this fact alone makes it more than probable that this place [Africa] is also likely where DE* emerged.

DE* is more common in Africa than outside of it -

It has been identified in African samples in more than one accasion in separately-conducted studies, having been identified in 5 Nigerian sampling candidates in one study, *1 in an Egyptian sample [see "Miscellaneous notes" below] and 1 Guinean individual in another . On the other hand, it had purportedly been identified in only 2 Tibetan sampling candidates. So we have 6 to 7 African cases vs. 2 Asian cases.

DE*'s internal phylogeny is more diverse and widely distributed in Africa -

Considering the greater internal phylogenetic branching of haplogroup E vs haplogroup D, it can be suggestive of either 1) longer time-depth for haplogroup E explosion/expansion, and hence, implicating DE* being around longer in Africa, as the homeland of haplogroup E ...

Or

2) that the haplogroup E lineage experienced an explosion that the D counterparts did not achieve in more or less the same time depth. The question becomes: What could account for this?

Either way, with fact being that African Hg E internal phylogeny is more elaborate than Hg D, the end result suggests that the intensity of such intra-E phylogenetic explosion seems to have had some level of erasing effect on DE* distribution. Given the greater pressure, due to greater demic explosion brought to bear on preexisting DE* in Africa — mainly by its own sub-phylogeny — than that which would have been the case in Asia by the YAP+ counterpart sub-phylogeny there, it's amazing that DE* is relentlessly visible enough in the African gene pool, as demonstrated by its greater chance detectability here than elsewhere, including Asia. This suggests that DE* would have been more widely distributed in Africa than in Asia, having been able to withstand greater pressure from greater subsequent demic expansion of Hg E phylogeny than that involving Hg D phylogeny, respectively in Africa and Asia.

The distribution and internal branching of Hg D suggests, on the other hand, that it involved lower scale dispersal of Hg D*, which were relatively more controlled in their subsequent expansion. The distribution pattern for instance, shows that the major subclades of D in different territories are highly differentiated and generally sharply geographically-structured, being confined to territorial spheres. At least that is the image reflected, if one goes by what's professed in theISOGG.org website, whatever may be said of the credibility:

Sub-group D1 (D-M15) is seen in Tibet, Mongolia, Central Asia, and Southeast Asia, and the sub-groups D* (D-M174) and D3 (D-P47) are seen in Central Asia. The sub-group D2 (D-M55) is seen almost exclusively in Japan.

Hg D* is presumably also identified in the Andaman Islands.

A hypothetical Hg DE* back-to-Africa migration seems to have been elusive in leaving genetic tracks behind, presumably from south Asia to Africa -

The supposed back-migrants would seem to have left no genetic tracks behind in a hypothetical destination from southern Asia via the Arabian peninsula, eastern Africa through to African interior, in a hypothetical back-to-Africa migration scenario. If they did, then it had been thoroughly erased by multiple demographic shifts. Hg D's distribution in south Asia, with rare to no presence in territories between that region and Africa, is however explained by founder effect of OOA migrants, already carrying Hg DE* amongst them.

Chandrasekar's speculation is highly questionable for the same reasons just stated above; see:

Some of the YAP insertion chromosomes without the M174 mutation reached the Mediterranean via Central Asia and gave rise to the E lineage with mutations at M40 and M96 (~31 000 years ago; Hammer et al. 1998). This E lineage back-migrated to Africa through the Levant as hypothesized by Hammer et al. (1997) and Altheide and Hammer (1997).

Hg D is rare to absent in the Levant, and conversely, Hg E is virtually rare to absent in populations that do carry Hg D.

Furthermore, Hg E's presence in the so-called Near East, including the Levant and Europe, serves as gene flow from Africa, because Africa is where the entire Hg E phylogeny occurs, not the Levant. All upstream Hg E markers are exclusively found in Africa, and essentially none in the Levant.

The so-called Near East has far much lower frequencies of Hg E than in mainland Africa, and all of these happen tobe subclades of African counterparts. Much of these subclades are relegated to the P2 (PN2) phylogeny. Upstream PN2 clades as generally known, only occur in Africa.

Revisiting Chandrasekar's post again,...

Some of the YAP insertion chromosomes without the M174 mutation reached the Mediterranean via Central Asia and gave rise to the E lineage with mutations at M40 and M96 (~31 000 years ago; Hammer et al. 1998).

It is also of note that Chandrasekar conveniently ignores that DE* has been found in Africa as well, but in even greater frequencies than his personal favored region [as noted in the second point above], i.e. Asia, not to mention that it is essentially non-existent in the so-called Mediterranean or the Levant. With DE* being in Africa, it is not necessary for Hg E to have come from the Levant, for reasons just mentioned and the ones immediately above this last Chandrasekar citation. Instead, Chandrasekar relies heavily on outdated studies, when Hg E phylogeny, as with many others, were in their early stages of being resolved.

His statement above, about "some of the YAP insertion chromosomes without the M174 mutation" has also implications that Chandrasekar seems to have overlooked:

Common sense intimates that any hypothetical DE* back-to-Africa migration — and it would have to have been major enough — would have been pooled from a newly situated migrant group. The keywords here: "newly situated".

Recalling Weale et al....

the presence of the DE* haplogroup has the effect of forcing an earlier date for the most recent common ancestor of all African YAP chromosomes. This reduces the possible time window within which a back-migration to Africa could have occurred under the scenario of an Asian origin for YAP. - Weale et al. 2003, Rare Deep-Rooting Y Chromosome Lineages in Humans.

Indeed! The presence of DE* in Africa suggests that this lineage was in place very shortly after its emergence. The OOA migrants had just recently left Africa for a reason; what on earth would these folks, who had just arrived, go back to Africa for, and at such a gruesomely long distance from a south Asian refuge? Pending tangible evidence of a compelling motive, it makes little sense.

And even if one were to take a hypothetical Asian origin of DE* for granted, based on skin pigmentation allele examinations, the original carriers of these markers would have closely resembled contemporary "black Africans", and even then, Hg E would still not be Asian [considering points above].

Let's face it; it's really not all that complicated: It just so happens that Hg D exists in Asia, while Hg E plays a dominating role in Africa, well, because DE* markers were present in both. Simple enough, isn't it?!

Neither territory has the other respective sub-clade lineage, because these emerged after OOA migrations, understandably.

Not sure why finding DE* therefore, surprises anyone. It's the only way D could have arrived in south Asia sans E; thus, DE* chromosomes brought in from Africa would have to have been around, in order for D to emerge, there is no other way around it. It is also the reason one finds DE* in both Africa, the origin point of destination, and Asia, the destination. However, instead of looking at it that way, some complicate things for themselves, and say that in order for DE* to be in Asia, it surely must have emerged there, and that there is no other way around that.

The most parsimonious explanation generally tends to reduce the number of questions for each answer that it provides than the alternative. In this case, an African origin entailing DE* dispersal in a OOA migration event, paving way for a founder effect situation in southern Asia is the most parsimonious. All things considered [from above], there really is little for the aforementioned sects to be cheerful about, at least from the intellectual side of things, as opposed to the religiously-motivated or plainly wishful end!
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Miscellaneous notes:

A lost gem?

The following recently grabbed the attention of the present author of this blog; the abstract goes like this:

The geographic location of Egypt, at the interface between North Africa, the Middle East, and southern Europe, prompted us to investigate the genetic diversity of this population and its relationship with neighboring populations. To assess the extent to which the modern Egyptian population reflects this intermediate geographic position, ten Unique Event Polymorphisms (UEPs), mapping to the nonrecombining portion of the Y chromosome, have been typed in 164 Y chromosomes from three North African populations. The analysis of these binary markers, which define 11 Y-chromosome lineages, were used to determine the haplogroup frequencies in Egyptians, Moroccan Arabs, and Moroccan Berbers and thereby define the Y-chromosome background in these regions. Pairwise comparisons with a set of 15 different populations from neighboring European, North African, and Middle Eastern populations and geographic analysis showed the absence of any significant genetic barrier in the eastern part of the Mediterranean area, suggesting that genetic variation and gene flow in this area follow the "isolation-by-distance" model. These results are in sharp contrast with the observation of a strong north-south genetic barrier in the western Mediterranean basin, defined by the Gibraltar Strait. Thus, the Y-chromosome gene pool in the modern Egyptian population reflects a mixture of European, Middle Eastern, and African characteristics, highlighting the importance of ancient and recent migration waves, followed by gene flow, in the region.

The piece has raised some questions as to whether the YAP+ chromosomes in "some East Asian populations, such as the Japanese and Tibetans" is the same one identified in the Egyptian sample, i.e. essentially "Hg D", since this is largely the only YAP+ type found in said groups. The answer: Not necessarily, since the authors tested for YAP+, which is shared between Hgs D and E. The Egyptian YAP+ was very likely a paraphyletic chromosome that did not test positive for Hg E*, you know, just like how Hg DE* is devoid of the downstream characteristic markers of Hg E*. The 12f2 marker tested here more than likely refers to Hg J, which in this journal is designated as Hg 9. The nomenclature used here is apparently outdated [after all, this is a 2002 study we're dealing with here], but the finding of an upstream YAP+ chromosome that didn't belong to Hg E (as denoted here by SRY8299) is interesting nonetheless, because it adds to that theme of the unparalleledrichness of Hg DE and derivatives on the African continent, as well as the distribution of the upstream DE* clade being *predominantly* an African 'thing'. So, in light of this, Egypt can now be added to the list of African territories wherein rare Hg DE* chromosome appears, a list which has no peers anywhere else where Hg DE* is concerned!

"haplogroup CF and DE molecular ancestors first evolved inside Africa and subsequently contributed as Y chromosome founders to pioneering migrations that successfully colonized Asia. While not proof, the DE and CF bifurcation (Figure 8d ) is consistent with independent colonization impulses possibly occurring in a short time interval."

Source: Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations

by Peter A. Underhill , Toomas Kivisild - 2007

A nutshell!...of what has essentially been more elaborately demonstrated about said markers on this site. The present author of this blog has not yet come across a single genetic journal that says differently about haplotype CF origin.

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